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Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides

Abstract

Comprehensive characterization of protein glycosylation is critical for understanding the structure and function of glycoproteins. However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. Here, we describe a chemoenzymatic method called solid phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) for the comprehensive characterization of glycoproteins that is able to determine glycan heterogeneity for individual glycosites in addition to providing information about the total N-linked glycan, glycosite-containing peptide and glycoprotein content of complex samples. The NGAG method can also be applied to quantitatively detect glycoprotein alterations in total and site-specific glycan occupancies.

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Figure 1: Workflow of solid-phase extraction of NGAG.
Figure 2: Extraction and identification of N-linked glycans and glycosite-containing peptides from OVCAR-3 cells using the NGAG method.
Figure 3: Quantification of glycans and glycosite-containing peptides in tunicamycin-treated OVCAR-3 cells.
Figure 4: Differential alterations of oligo-mannose glycans in tunicamycin-treated OVCAR-3 cells.

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Acknowledgements

This work was supported by the National Institutes of Health, National Cancer Institute, Clinical Proteomic Tumor Analysis Consortium (U24CA160036), the Early Detection Research Network (EDRN, U01CA152813 and U24CA115102) and R01CA112314, and by the National Institutes of Health, National Heart, Lung, and Blood Institute Programs of Excellence in Glycosciences (PEG, P01HL107153) and the Johns Hopkins Proteomics Center (N01-HV-00240).

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Authors

Contributions

S.S. and H.Z. prepared the manuscript with contributions from all co-authors; S.S. conducted most experimental and data analyses with support from other co-authors; P.S. performed part of mass spectrometric analyses; P.S. and W.Y. contributed to part of data analyses; S.T.E. developed software for intact glycopeptide analysis; N.T. and N.H. cultured cells; S.Y. and P.A. contributed to part of the glycan analysis experiments; L.C. assisted in some of sample preparation experiments; D.W.C. and Z.Z. provided additional research support.

Corresponding author

Correspondence to Hui Zhang.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 The timeline of the NGAG method for extraction of N-linked glycans and glycosite-containing peptides.

The timeline can be changed based on the number of samples.

Supplementary Figure 2 Identification of N-linked glycans, glycosite-containing peptides, and intact glycopeptides from bovine fetuin using the NGAG method.

(a) MALDI-TOF-MS spectrum of fetuin glycans. The possible glycan structures of the top 13 peaks are shown in the spectrum. (b) MS/MS spectrum of a glycosite (Asn156)-containing fetuin peptide. (c) MS/MS spectrum of an intact glycopeptide at glycosite Asn156 with a HexNAc5Hex6 (N5H6) glycan attached. Oxonium ions (highlighted in green) were used to select the glycopeptide spectra from the global data, and the accurate masses of the precursor ion and peptide+HexNAc/peptide (highlighted in blue) fragment ions as well as b/y fragment ions were used to identify the intact glycopeptide. (d) Site-specific heterogeneity of bovine fetuin. N: HexNAc; H: Hexose; F: Fucose; A: Sialic acid. The intact glycopeptides were identified from triplicate LC-MS/MS analysis.

Supplementary Figure 3 MS/MS spectra of the glycosite-containing peptides (deglycosylated peptides) identified from bovine fetuin.

(a) The peptide N#CSVR with glycosite 99. (b) The peptide N#DSR with glycosite 156. “.” indicates the cleavage site by trypsin. The LC-MS/MS data was analyzed by Proteome Discoverer software (Thermo Fisher Scientific) allowing trypsin (semi) as the enzyme and at least 4 amino acids for peptide identification.

Supplementary Figure 4 MALDI-TOF-MS spectra of N-glycans isolated from OVCAR-3 cells using NGAG and the possible N-glycan structures with the composition matched to the glycan masses.

Supplementary Figure 5 The detection of glycans with 1Da mass difference by LC-MS using a Q-Exactive mass spectrometer.

Two pairs of glycans with 1Da mass difference were used as the examples. These glycans with 1Da differences can be clearly distinguished based on their isotopic masses and retention time (which are mainly determined by the number of aniline-modified sialic acids) in LC-MS analysis.

Supplementary Figure 6 Quantification of glycosite-containing peptides between duplicate NGAG isolations.

Supplementary Figure 7 Reproducible analyses of N-glycans and glycosites using the NGAG method.

(a) The number of identified glycans from three NGAG isolations. Each glycan sample was analyzed once by LC-MS/MS. (b) Label-free quantification of the identified glycans between two isolations from the same amount of fetuin. (c) Relative quantification of glycosite-containing peptides (iTRAQ labeling method) isolated from different amounts of fetuin. (d) Label-free quantification of intact glycopeptides between replicate analyses of tryptic peptides from fetuin. (e) Comparison of identified OVCAR-3 cell glycans among three NGAG isolations. (f) Comparison of identified glycosite-containing peptides from OVCAR-3 cells among three NGAG isolations. (g) Comparison of identified glycosite-containing peptides among three LC-MS/MS injection of the same sample isolated from OVCAR-3 cells. Each glycan or glycosite-containing peptide sample was analyzed once by LC-MS/MS.

Supplementary Figure 8 Liquid chromatography profiles of the glycans of OVCAR-3 cells from triplicate isolations using the NGAG method.

The base peak profiles of the raw files of the triplicate isolations are displayed in Xcalibur.

Supplementary Figure 9 Liquid chromatography profiles of glycosite-containing peptides of OVCAR-3 cells from (a) 3 LC-MS/MS replicates and (b) 3 isolation replicates using the NGAG method.

The base peak profiles of the raw files of triplicate isolations are displayed in Xcalibur.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–9 (PDF 4044 kb)

Supplementary Text and Figures

Supplementary Results and Discussion, Supplementary Figures 1–9 and Supplementary Table 8 (PDF 2500 kb)

Supplementary Table 1

N-linked glycan compositions detected from bovine fetuin using NGAG method (XLSX 21 kb)

Supplementary Table 2

Intact N-glycopeptides identified from the global data of bovine fetuin (XLSX 24 kb)

Supplementary Table 3

N-linked glycan compositions detected from OVCAR-3 cells using NGAG method (XLSX 20 kb)

Supplementary Table 4

N-Linked glycosite-containing peptides identified from OVCAR-3 cells using NGAG method (XLSX 207 kb)

Supplementary Table 5

N-Linked glycosite-containing peptides identified from OVCAR-3 cells using SPEG method (XLSX 137 kb)

Supplementary Table 6

All N-linked glycosite-containing peptides identified from OVCAR-3 cells using NGAG and SPEG methods (XLSX 395 kb)

Supplementary Table 7

Intact N-glycopeptides identified from HILIC enriched glycopeptides from OVCAR-3 cells (1X FDR) (XLSX 435 kb)

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Sun, S., Shah, P., Eshghi, S. et al. Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides. Nat Biotechnol 34, 84–88 (2016). https://doi.org/10.1038/nbt.3403

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